It is possible to provide support for multiple, identical seqservice.netPathPrefixSearch property values. This is achieved by using the seqservice.eventFileDirsToUseForSearchReplacePair properties. These properties can be used to specify the mappings between search replace pairs and their associated event directories.

• The value of the seqservice.eventFileDirsToUseForSearchReplacePair property is a comma-separated list of event file directory suffixes to be applied to the search/replace pair.

• If the property is not supplied (or the value is left empty), the behavior is unchanged. In this case, the search/replace pair is treated as global and applied to all active event file directory suffixes.

The following example uses a MiSeq installation to show several configuration options, with comments. Similar configuration may be applied for installations of other Illumina instrument integrations (eg, MiSeqDx, NextSeq).

Note that the last part of this example shows configuration that results in an error.

Custom Field/User-Defined Field

As of Clarity LIMS v5.0.0, the term user-defined field (UDF) has been replaced with custom field in the user interface. However, the API resource is still called UDF.

There are two types of custom fields:

• Master step fields — Configured on master steps. Master step fields only apply to the following:

  • The master step on which the fields are configured.

  • The steps derived from those master steps.

• Global fields — Configured on entities (eg, submitted sample, derived sample, measurement, etc.). Global fields apply to the entire Clarity LIMS system.

Run Mode

• Samplesheet run mode - Only the sample sheet is generated and stored on Clarity LIMS. Run/Analysis configuration is imported manually into the instrument via a sample sheet to start the run. The downstream secondary analysis is performed on-premise. In NextSeq 1000/2000, this mode is also known as the Local Mode.

• Hybrid/Cloud run mode - The planned run is created on ICA based on the run/analysis data from the integration service. The planned run contains all the run and analysis configuration required to start the run on the instrument. The sample sheet is also generated and stored on Clarity LIMS for reference purposes. In Cloud run mode, the analysis is performed on the cloud whereas in Hybrid run mode, the analysis is performed on-premise.

To support planned run creation for samples having duplicate names with different indexes, updates are required on the library preparation workflow that these samples go through.

Follow these steps to update the output Naming Convention of the library preparation workflow.

1. Select the Configuration tab, and then select the Lab Work tab.

2. Under Master Steps, select the master step of the library preparation workflow (e.g., Library Prep Validation).

Compatibility:

• Clarity LIMS v5.1 & later, with NGS Extensions v5.17 and later

Use the Template File Generator tool to generate custom sample sheets for upload to Illumina instruments.

The driver_file_generator script is invoked in an automation command line, typically configured on the step prior to the instrument run. By default, the automation is triggered by a button on the Record Details screen.

For details on the parameters used by the script, template file contents, and how to create custom template files, see the Template File Generator documentation.

MiSeq Control Software and bcl2fastq2-compatible sample sheet template files are available from the Clarity LIMS Support team.

MiSeq Sample Sheet Generation

This section summarizes the default configuration for MiSeq sample sheet generation. A template file that is compatible with MiSeq Control Software (MCS) is attached to this page.

¹ The version reflected in the master step may be different depending on the integration version you are using.

Automation command line:

For a description of the parameters used by the driver_file_generator script, see the article.

In Clarity LIMS v5.1 and later, the automation is configured on the Automation configuration screen. By default, the automation is triggered by a manual button on the Record Details screen. The automation trigger settings are configured on the master step configuration screen.

bcl2fastq2 Sample Sheet Generation

This section summarizes the default configuration for bcl2fastq2 sample sheet generation.

Two bcl2fastq2 software-compatible template files are attached to this page. If you would like reverse complement sequences to be included in your sample sheet, use the BCL2FASTQ_Reverse_Complement_Samplesheet.csv template.

¹ The version reflected in the master step may be different depending on the integration version you are using.

Automation command line:

or a description of the parameters used by the driver_file_generator script, see the article.

In Clarity LIMS v5.1 and later, the automation is configured on the Automation configuration screen. By default, the automation is triggered by a manual button on the Record Details screen. The automation trigger settings are configured on the master step configuration screen.

Custom File Generation

To generate a custom sample sheet, complete the following steps:

1. Download the desired template. (See section below.)

2. Customize the template file as required. (See documentation.)

3. Upload the customized template file to the appropriate step automation.

For instructions on uploading template files to an automation, and adding the token to the command line, see the following articles:

• Adding & Configuring Automations (Attaching template files to step automations document section) in the .

Attachments

MiSeqSamplesheetv3.csv:

BCL2FASTQ_Samplesheet.csv:

BCL2FASTQ_Reverse_Complement_Samplesheet.csv:

In Clarity file-based integrations such as NextSeq 500/550, there may be a need for file transfer between hosted Clarity LIMS instance and Customer File Server.

Examples of file transfer scenarios:

• Transfer of sample sheet from Clarity LIMS instance to Customer File Server

• Transfer of sequencing/analysis run data from Customer File Server to Clarity LIMS instance

Rsync-based File Transfer

Rsync can be used as an alternative to VPN for transferring files between Clarity LIMS instance and Customer File Server. Rsync is a command-line tool to copy and synchronize files and directories between two locations and leverages SSH network protocol through port 22.

Prerequisites

1. Same version of Rsync should be installed on both Clarity LIMS instance and Customer File Server.

   • Install Rsync by running either commands as root user:

   • Check the rsync version and protocol version:

Command

• Transfer file from customer file server to Clarity LIMS instance.

  {% hint style="danger" %} The destination directory to transfer the file must exist in the Clarity LIMS instance and the user must have write permissions to this directory. {% endhint %}

• Transfer file from Clarity LIMS instance to customer file server.

  {% hint style="danger" %} The file to transfer must exist in the Clarity LIMS instance and the executing user must have read permissions to the source directory containing the file and the file itself. {% endhint %}

Refer to for detailed information on rsync

Example

transfer_samplesheet.sh:

transfer_run_data.sh:

Data Clean Up

cleanup_rundata.sh:

Automated Bash Script

Crontab can be used to automatically schedule bash scripts to run at a given set interval.

Example

1. Run the following command to open and edit the current cron jobs for the current user.

2. Add the following lines to run the transfer scripts every 15 minutes.

3. Add the following lines to run the clean up script every Sunday at midnight.